Make LIMMA comparisons

Description

Make LIMMA comparisons

Usage

makeLimmaComp(expr, design, cont.matrix)

Arguments

Value

A list with one data.frame per comparison

Examples

## Not run: 
# Create a mock expressionset to test functions
      mockexpset <- matrix(rnorm(15000), ncol = 15)
      colnames(mockexpset) <- paste0('GSM', seq(1, 15))
      set.seed(100)
      rownames(mockexpset) <- apply(replicate(n = 1000, sample(letters, 8)),
                                  2, function(x) paste(x, collapse = ''))
      sample_annot <- data.frame(geo_accession = colnames(mockexpset),
                               group = c(rep('skin_healthy', 5), rep('degree1', 5),
                                         rep('degree2', 5)),
                               subject = paste0('S', c(rep(1:5),rep(1:5), rep(1:5))))
# Testing function below
      # Paired
      cont_mat1 <- makeContMatrix(class_column = 'group', which_groups = c('degree1', 'degree2'),
                                 comp_group = 'skin_healthy', subject_col= 'subject',
                                 sample_annot = sample_annot, expr = mockexpset)
      limma_result1 <- do.call(makeLimmaComp, cont_mat1)
      # Unpaired
      cont_mat2 <- makeContMatrix(class_column = 'group', which_groups = c('degree1', 'degree2'),
                                 comp_group = 'skin_healthy', sample_annot = sample_annot,
                                 expr = mockexpset)
      limma_result2 <- do.call(makeLimmaComp, cont_mat2)

## End(Not run)